A synchrotron X-ray study of the electron density in C-type rare earth oxides

1996 ◽  
Vol 52 (3) ◽  
pp. 414-422 ◽  
Author(s):  
E. N. Maslen ◽  
V. A. Streltsov ◽  
N. Ishizawa
Keyword(s):  
Heavy Metal ◽  
Rare Earth ◽  
Electron Density ◽  
Approximate Symmetry ◽  
Data Set ◽  
X Ray ◽  
Metal Atoms ◽  
Structure Factors ◽  
Deformation Electron Density ◽  
Synthetic Crystals

Structure factors for small synthetic crystals of the C-type rare earth (RE) sesquioxides Y2O3, Dy2O3 and Ho2O3 were measured with focused λ = 0.7000 (2) Å, synchrotron X-radiation, and for Ho2O3 were re-measured with an MoKα (λ = 0.71073 Å) source. Approximate symmetry in the deformation electron density (Δρ) around a RE atom with pseudo-octahedral O coordination matches the cation geometry. Interactions between heavy metal atoms have a pronounced effect on the Δρ map. The electron-density symmetry around a second RE atom is also perturbed significantly by cation–anion interactions. The compounds magnetic properties reflect this complexity. Space group Ia{\bar 3}, cubic, Z = 16, T = 293 K: Y2O3, Mr = 225.82, a = 10.5981 (7) Å, V = 1190.4 (2) Å3, Dx = 5.040 Mg m−3, μ 0.7 = 37.01 mm−1, F(000) = 1632, R = 0.067, wR = 0.067, S = 9.0 (2) for 1098 unique reflections; Dy2O3, Mr = 373.00, a = 10.6706 (7) Å, V = 1215.0 (2) Å3, Dx = 8.156 Mg m−3, μ 0.7 = 44.84 mm−1, F(000) = 2496, R = 0.056, wR = 0.051, S = 7.5 (2) for 1113 unique reflections; Ho2O3, Mr = 377.86, a = 10.606 (2) Å, V = 1193.0 (7) Å3, Dx = 8.415 Mg m−3, μ 0.7 = 48.51 mm−1 F(000) = 2528, R = 0.072, wR = 0.045, S = 9.2 (2) for 1098 unique reflections of the synchrotron data set.

Synchrotron X-ray study of Er3Al5O12 and Yb3Al5O12 garnets

2001 ◽  
Vol 57 (2) ◽  
pp. 136-141 ◽  
Author(s):  
Barbara Etschmann ◽  
Victor Streltsov ◽  
Nobuo Ishizawa ◽  
E. N. Maslen
Keyword(s):  
Rare Earth ◽  
Electron Density ◽  
Relative Position ◽  
Nearest Neighbor ◽  
Difference Electron Density ◽  
X Ray ◽  
Density Maps ◽  
Structure Factors ◽  
The Difference ◽  
The Rare Earth

Structure factors for Er3Al5O12 and Yb3Al5O12 garnets were measured using focused synchrotron X-radiation, with λ = 0.7500 (2) and 0.7000 (2) Å, respectively. The difference electron density maps for Er3Al5O12 and Yb3Al5O12 were similar, as expected. This was attributed to the 4f electrons being shielded, which reduces their effectiveness in chemical bonding and the relative position of the rare-earth atoms in the periodic table. The symmetry of the difference electron density around the rare-earth atoms was found to reflect that of the cation geometry, emphasizing the importance of second nearest-neighbor interactions. This is consistent with the view that oxide-type structures may be regarded as a packed array of cations with anions in the interstices.

Synchrotron X-ray analysis of the electron density in HoFe2

1999 ◽  
Vol 55 (3) ◽  
pp. 321-326 ◽  
Author(s):  
Victor A. Streltsov ◽  
Nobuo Ishizawa
Keyword(s):  
Electron Density ◽  
Magnetic Order ◽  
Avalanche Photodiode ◽  
Spin Coupling ◽  
Coupling Mechanism ◽  
Significant Excess ◽  
X Ray ◽  
Structure Factors ◽  
Exchange Repulsion ◽  
Deformation Electron Density

Structure factors for a small holmium diiron HoFe2 Laves crystal were measured with focused λ = 0.75 Å synchrotron X-radiation using a fast avalanche photodiode (APD) counter. The deformation electron density (Δρ) maps are remarkable for significant excess electron density midway between the Ho atoms, which is not dissimilar to the peaks attributed to classic `covalent bonding' in C and Si crystals. These residual electrons accumulate at the centres of the kagomé net hexagons and form, with the Fe atoms, a triangular lattice which is characterized by more stable magnetic order than the kagomé net. Similar peaks occur along the Ho–Fe and Fe–Fe contacts. These results confirm the hypothesis that 5d electrons of the rare-earth atoms are important in the spin-coupling mechanism for HoFe2-type compounds. The 5d electrons are far less localized than the 4f electrons, and considerable 5d–5d and 5d–3d orbital overlap occurs between neighbouring atoms. Aspherical electron density near the Ho nuclei can be associated with the Ho 4f subshell electrons. Strong depletions of the Δρ near the atoms along the Ho–Ho, Ho–Fe and Fe–Fe vectors are indications of exchange repulsion. The effect of anharmonicity on the Δρ is insignificant.

Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-nitroimidazole: an experimental and theoretical study

2016 ◽  
Vol 72 (5) ◽  
pp. 775-786 ◽  
Author(s):  
Chinnasamy Kalaiarasi ◽  
Mysore S Pavan ◽  
Poomani Kumaradhas
Keyword(s):  
Electron Density ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Topological Characterization ◽  
Data Set ◽  
X Ray ◽  
Charge Concentration

An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen–Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density ρbcp(r) and the Laplacian of electron density ∇2ρbcp(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed usingCRYSTAL09.

Multipole electron densities and atomic displacement parameters in urea from accurate powder X-ray diffraction

2019 ◽  
Vol 75 (4) ◽  
pp. 600-609 ◽  
Author(s):  
Bjarke Svane ◽  
Kasper Tolborg ◽  
Lasse Rabøl Jørgensen ◽  
Martin Roelsgaard ◽  
Mads Ry Vogel Jørgensen ◽  
...  
Keyword(s):  
Electron Density ◽  
Molecular System ◽  
Atomic Displacement ◽  
High Symmetry ◽  
X Ray Diffraction ◽  
High Quality ◽  
Acta Cryst ◽  
X Ray ◽  
Density Determination ◽  
Structure Factors

Electron density determination based on structure factors obtained through powder X-ray diffraction has so far been limited to high-symmetry inorganic solids. This limit is challenged by determining high-quality structure factors for crystalline urea using a bespoke vacuum diffractometer with imaging plates. This allows the collection of data of sufficient quality to model the electron density of a molecular system using the multipole method. The structure factors, refined parameters as well as chemical bonding features are compared with results from the high-quality synchrotron single-crystal study by Birkedalet al.[Acta Cryst.(2004), A60, 371–381] demonstrating that powder X-ray diffraction potentially provides a viable alternative for electron density determination in simple molecular crystals where high-quality single crystals are not available.

scholarly journals Transferability of Multipole Charge-Density Parameters: Application to Very High Resolution Oligopeptide and Protein Structures

1998 ◽  
Vol 54 (6) ◽  
pp. 1306-1318 ◽  
Author(s):  
Christian Jelsch ◽  
Virginie Pichon-Pesme ◽  
Claude Lecomte ◽  
André Aubry
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Diffraction Data ◽  
Protein Structures ◽  
Fourier Synthesis ◽  
Covalent Bonds ◽  
X Ray ◽  
Density Peaks ◽  
Deformation Electron Density ◽  
Temperature Factors

Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron density (parameterized as multipoles) and of the atomic charges. This fine description of the electron density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole parameters. A database of such parameters has been built from charge-density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-density multipole parameters have been transferred and the X-ray structure of a 3_{10} helix octapeptide Ac-Aib_2-L-Lys(Bz)-Aib_2-L-Lys(Bz)-Aib_2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 Å at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (\Delta B ≃ 0.4 Å2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement parameters. The contribution to the diffraction of the different components of the electron density has also been analyzed. This analysis indicates that the electron-density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 Å^2). In this case, a non-truncated Fourier synthesis of the deformation density requires that the diffraction data are available to a resolution better than 0.9 Å.

scholarly journals Electron density of a new EGFR Tyrokinase-inhibitor at 100 K, consideration of different models

2008 ◽  
Vol 223 (8) ◽  
Author(s):  
Stefan Mebs ◽  
Anja Lüth ◽  
Wolfgang Löwe ◽  
Carsten Paulmann ◽  
Peter Luger
Keyword(s):  
High Resolution ◽  
Synchrotron Radiation ◽  
Electron Density ◽  
Electron Shell ◽  
Cancer Drug ◽  
Outer Electron ◽  
Data Set ◽  
X Ray ◽  
Atomic Properties ◽  
Anti Cancer

AbstractThe electron density (ED) of a substituted 4-(indol-3-yl)-quinazoline, a newly developed anti-cancer drug, was determined from a high resolution X-ray data set measured at 100 K using synchrotron radiation. Because the structure contains a chlorine atom, which has a diffuse outer electron shell and is therefore beyond standard modeling, the influence of the model on the bond topological and atomic properties was studied following Bader's approach of ‘Atoms In Molecules’ (AIM). The expansion/contraction parameters

Accurate charge densities from powder X-ray diffraction – a new version of the Aarhus vacuum imaging-plate diffractometer

2017 ◽  
Vol 73 (4) ◽  
pp. 521-530 ◽  
Author(s):  
Kasper Tolborg ◽  
Mads R. V. Jørgensen ◽  
Sebastian Christensen ◽  
Hidetaka Kasai ◽  
Jacob Becker ◽  
...  
Keyword(s):  
Electron Density ◽  
High Energy ◽  
Imaging Plate ◽  
High Symmetry ◽  
X Rays ◽  
X Ray Diffraction ◽  
Core Electron ◽  
X Ray ◽  
Peak Broadening ◽  
Structure Factors

In recent years powder X-ray diffraction has proven to be a valuable alternative to single-crystal X-ray diffraction for determining electron-density distributions in high-symmetry inorganic materials, including subtle deformation in the core electron density. This was made possible by performing diffraction measurements in vacuum using high-energy X-rays at a synchrotron-radiation facility. Here we present a new version of our custom-built in-vacuum powder diffractometer with the sample-to-detector distance increased by a factor of four. In practice this is found to give a reduction in instrumental peak broadening by approximately a factor of three and a large improvement in signal-to-background ratio compared to the previous instrument. Structure factors of silicon at room temperature are extracted using a combined multipole–Rietveld procedure and compared withab initiocalculations and the results from the previous diffractometer. Despite some remaining issues regarding peak asymmetry, the new diffractometer yields structure factors of comparable accuracy to the previous diffractometer at low angles and improved accuracy at high angles. The high quality of the structure factors is further assessed by modelling of core electron deformation with results in good agreement with previous investigations.

A First Experimental Electron Density Study on a C70 Fullerene: (C70C2F5)10

2010 ◽  
Vol 65 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Roman Kalinowski ◽  
Manuela Weber ◽  
Sergey I. Troyanov ◽  
Carsten Paulmann ◽  
Peter Luger
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Theoretical Calculations ◽  
Asymmetric Unit ◽  
Data Set ◽  
X Ray ◽  
Atomic Properties ◽  
Density Methods ◽  
Experimental Electron Density ◽  
Density Study

The electron density of the C70 fullerene C70(C2F5)10 was determined from a high-resolution X-ray data set measured with synchrotron radiation (beamline F1 of Hasylab/DESY, Germany) at a temperature of 100 K. With 140 atoms in the asymmetric unit this fullerene belongs to the largest problems examined until now by electron density methods. Using the QTAIM formalism quantitative bond topological and atomic properties have been derived and compared with the results of theoretical calculations on the title compound and on free C70

scholarly journals A chemical interpretation of protein electron density maps in the worldwide protein data bank

2019 ◽  
Author(s):  
Sen Yao ◽  
Hunter N.B. Moseley
Keyword(s):  
Protein Data Bank ◽  
Electron Density ◽  
Structural Model ◽  
Data Bank ◽  
X Ray ◽  
New Methods ◽  
Link Type ◽  
Density Maps ◽  
Structure Factors ◽  
Python Package

AbstractHigh-quality three-dimensional structural data is of great value for the functional interpretation of biomacromolecules, especially proteins; however, structural quality varies greatly across the entries in the worldwide Protein Data Bank (wwPDB). Since 2008, the wwPDB has required the inclusion of structure factors with the deposition of x-ray crystallographic structures to support the independent evaluation of structures with respect to the underlying experimental data used to derive those structures. However, interpreting the discrepancies between the structural model and its underlying electron density data is difficult, since derived electron density maps use arbitrary electron density units which are inconsistent between maps from different wwPDB entries. Therefore, we have developed a method that converts electron density values into units of electrons. With this conversion, we have developed new methods that can evaluate specific regions of an x-ray crystallographic structure with respect to a physicochemical interpretation of its corresponding electron density map. We have systematically compared all deposited x-ray crystallographic protein models in the wwPDB with their underlying electron density maps, if available, and characterized the electron density in terms of expected numbers of electrons based on the structural model. The methods generated coherent evaluation metrics throughout all PDB entries with associated electron density data, which are consistent with visualization software that would normally be used for manual quality assessment. To our knowledge, this is the first attempt to derive units of electrons directly from electron density maps without the aid of the underlying structure factors. These new metrics are biochemically-informative and can be extremely useful for filtering out low-quality structural regions from inclusion into systematic analyses that span large numbers of PDB entries. Furthermore, these new metrics will improve the ability of non-crystallographers to evaluate regions of interest within PDB entries, since only the PDB structure and the associated electron density maps are needed. These new methods are available as a well-documented Python package on GitHub and the Python Package Index under a modified Clear BSD open source license.Author summaryElectron density maps are very useful for validating the x-ray structure models in the Protein Data Bank (PDB). However, it is often daunting for non-crystallographers to use electron density maps, as it requires a lot of prior knowledge. This study provides methods that can infer chemical information solely from the electron density maps available from the PDB to interpret the electron density and electron density discrepancy values in terms of units of electrons. It also provides methods to evaluate regions of interest in terms of the number of missing or excessing electrons, so that a broader audience, such as biologists or bioinformaticians, can also make better use of the electron density information available in the PDB, especially for quality control purposes.Software and full results available athttps://github.com/MoseleyBioinformaticsLab/pdb_eda (software on GitHub)https://pypi.org/project/pdb-eda/ (software on PyPI)https://pdb-eda.readthedocs.io/en/latest/ (documentation on ReadTheDocs)https://doi.org/10.6084/m9.figshare.7994294 (code and results on FigShare)

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